Contig_AMOS.hh

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#ifndef __Contig_AMOS_HH
#define __Contig_AMOS_HH 1

#include "Sequence_AMOS.hh"
#include "Layout_AMOS.hh"
#include <vector>




namespace AMOS {

//================================================ Contig_t ====================
//==============================================================================
class Contig_t : public Sequence_t
{
  
private:

  std::vector<Pos_t> gaps_m;          
  std::vector<Tile_t> reads_m;        


  //--------------------------------------------------- compress ---------------
  void compress ( );


  //--------------------------------------------------- uncompress -------------
  void uncompress ( );


protected:

  //--------------------------------------------------- readRecord -------------
  virtual void readRecord (std::istream & fix, std::istream & var);


  //--------------------------------------------------- writeRecord ------------
  virtual void writeRecord (std::ostream & fix, std::ostream & var) const;


public:

  static const NCode_t NCODE;


  //--------------------------------------------------- Contig_t ---------------
  Contig_t ( )
  {

  }


  //--------------------------------------------------- Contig_t ---------------
  Contig_t (const Contig_t & source)
  {
    *this = source;
  }


  //--------------------------------------------------- ~Contig_t --------------
  ~Contig_t ( )
  {

  }


  //--------------------------------------------------- clear ------------------
  virtual void clear ( )
  {
    Sequence_t::clear( );
    gaps_m . clear( );
    reads_m . clear( );
  }


  //--------------------------------------------------- gap2ungap --------------
  Pos_t gap2ungap (Pos_t gap) const;


  //--------------------------------------------------- ungap2gap --------------
  Pos_t ungap2gap (Pos_t ungap) const;


  //--------------------------------------------------- getNCode ---------------
  virtual NCode_t getNCode ( ) const
  {
    return Contig_t::NCODE;
  }


  //--------------------------------------------------- getReadTiling ----------
  const std::vector<Tile_t> & getReadTiling ( ) const
  {
    return reads_m;
  }


  //--------------------------------------------------- getReadTiling ----------
  std::vector<Tile_t> & getReadTiling ( )
  {
    return reads_m;
  }


  //--------------------------------------------------- getSpan ----------------
  Size_t getSpan ( ) const;


  //--------------------------------------------------- getUngappedLength ------
  Size_t getUngappedLength ( ) const;


  //--------------------------------------------------- getUngappedQualString --
  std::string getUngappedQualString ( ) const
  {
    return getUngappedQualString (Range_t (0, getLength( )));
  }


  //--------------------------------------------------- getUngappedQualString --
  std::string getUngappedQualString (Range_t range) const;


  //--------------------------------------------------- getUngappedSeqString ---
  std::string getUngappedSeqString ( ) const
  {
    return getUngappedSeqString (Range_t (0, getLength( )));
  }


  //--------------------------------------------------- getUngappedSeqString ---
  std::string getUngappedSeqString (Range_t range) const;


  //--------------------------------------------------- readMessage ------------
  virtual void readMessage (const Message_t & msg);


  //--------------------------------------------------- readUMD ----------------
  bool readUMD (std::istream & in);


  //--------------------------------------------------- setReadTiling ----------
  void setReadTiling (const std::vector<Tile_t> & reads)
  {
    reads_m = reads;
  }


  //--------------------------------------------------- setReadTiling ----------
  void setReadTiling (const Layout_t & layout)
  {
    reads_m = layout . getTiling( );
  }


  //--------------------------------------------------- writeMessage -----------
  virtual void writeMessage (Message_t & msg) const;


  //--------------------------------------------------- writeUMD ---------------
  void writeUMD (std::ostream & out) const;

};

} // namespace AMOS

#endif // #ifndef __Contig_AMOS_HH

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